A new computational method to split large biochemical networks into coherent subnets

<p>Abstract</p> <p>Background</p> <p>Compared to more general networks, biochemical networks have some special features: while generally sparse, there are a small number of highly connected metabolite nodes; and metabolite nodes can also be divided into two classes: internal nodes with associated mass balance constraints and external ones without. Based on these features, reclassifying selected internal nodes (separators) to external ones can be used to divide a large complex metabolic network into simpler subnetworks. Selection of separators based on node connectivity is commonly used but affords little detailed control and tends to produce excessive fragmentation.</p> <p>The method proposed here (Netsplitter) allows the user to control separator selection. It combines local connection degree partitioning with global connectivity derived from random walks on the network, to produce a more even distribution of subnetwork sizes. Partitioning is performed progressively and the interactive visual matrix presentation used allows the user considerable control over the process, while incorporating special strategies to maintain the network integrity and minimise the information loss due to partitioning.</p> <p>Results</p> <p>Partitioning of a genome scale network of 1348 metabolites and 1468 reactions for <it>Arabidopsis thaliana </it>encapsulates 66% of the network into 10 medium sized subnets. Applied to the flavonoid subnetwork extracted in this way, it is shown that Netsplitter separates this naturally into four subnets with recognisable functionality, namely synthesis of lignin precursors, flavonoids, coumarin and benzenoids. A quantitative quality measure called <it>efficacy </it>is constructed and shows that the new method gives improved partitioning for several metabolic networks, including bacterial, plant and mammal species.</p> <p>Conclusions</p> <p>For the examples studied the Netsplitter method is a considerable improvement on the performance of connection degree partitioning, giving a better balance of subnet sizes with the removal of fewer mass balance constraints. In addition, the user can interactively control which metabolite nodes are selected for cutting and when to stop further partitioning as the desired granularity has been reached. Finally, the blocking transformation at the heart of the procedure provides a powerful visual display of network structure that may be useful for its exploration independent of whether partitioning is required.</p

Genes involved in ethylene and gibberellins metabolism are required for endosperm-limited germiantion of Sisymbrium officinales L. Seeds

The rupture of the seed coat and that of the endosperm were found to be two sequential events in the germination of Sisymbrium officinale L. seeds, and radicle protrusion did not occur exactly in the micropylar area but in the neighboring zone. The germination patterns were similar both in the presence of gibberellins (GA4+7) and in presence of ethrel. The analysis of genes involved in GAs synthesis and breakdown demonstrated that (1) SoGA2ox6 expression peaked just prior to radicle protrusion (20–22 h), while SoGA3ox2 and SoGA20ox2 expression was high at early imbibition (6 h) diminishing sharply thereafter; (2) the accumulation of SoGA20ox2 transcript was strongly inhibited by paclobutrazol (PB) as well as by inhibitors of ET synthesis and signaling (IESS) early after imbibition (6 h), while SoGA3ox2 and SoGA2ox6 expression was slowly depressed as germination progressed; (3) ethrel and GA4+7 positively or negatively affected expression of SoGA3ox2, SoGA20ox2, and SoGA2ox6, depending on the germination period studied. Regarding genes involved in ET synthesis, our results showed that SoACS7 was expressed, just prior to radicle emergence while SoACO2 expression slowly increased as germination progressed. Both genes were strongly inhibited by PB but were almost unaffected by externally added ethrel or GA4+7. These results suggest that GAs are more important than ET during the early stages of imbibition, while ET is more important at the late phases of germination of S. officinale L. seed

Clinical course and prognosis of musculoskeletal pain in patients referred for physiotherapy: does pain site matter?

Background: Danish patients with musculoskeletal disorders are commonly referred for primary care physiotherapy treatment but little is known about their general health status, pain diagnoses, clinical course and prognosis. The objectives of this study were to 1) describe the clinical course of patients with musculoskeletal disorders referred to physiotherapy, 2) identify predictors associated with a satisfactory outcome, and 3) determine the influence of the primary pain site diagnosis relative to those predictors. Methods: This was a prospective cohort study of patients (n = 2,706) newly referred because of musculoskeletal pain to 30 physiotherapy practices from January 2012 to May 2012. Data were collected via a web-based questionnaire 1–2 days prior to the first physiotherapy consultation and at 6 weeks, 3 and 6 months, from clinical records (including primary musculoskeletal symptom diagnosis based on the ICPC-2 classification system), and from national registry data. The main outcome was the Patient Acceptable Symptom State. Potential predictors were analysed using backwards step-wise selection during longitudinal Generalised Estimating Equation regression modelling. To assess the influence of pain site on these associations, primary pain site diagnosis was added to the model. Results: Of the patients included, 66% were female and the mean age was 48 (SD 15). The percentage of patients reporting their symptoms as acceptable was 32% at 6 weeks, 43% at 3 months and 52% at 6 months. A higher probability of satisfactory outcome was associated with place of residence, being retired, no compensation claim, less frequent pain, shorter duration of pain, lower levels of disability and fear avoidance, better mental health and being a non-smoker. Primary pain site diagnosis had little influence on these associations, and was not predictive of a satisfactory outcome. Conclusion: Only half of the patients rated their symptoms as acceptable at 6 months. Although satisfactory outcome was difficult to predict at an individual patient level, there were a number of prognostic factors that were associated with this outcome. These factors should be considered when developing generic prediction tools to assess the probability of satisfactory outcome in musculoskeletal physiotherapy patients, because the site of pain did not affect that prognostic association

Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network

The cuticle covering plants' aerial surfaces is a unique structure that plays a key role in organ development and protection against diverse stress conditions. A detailed analysis of the tomato colorless-peel y mutant was carried out in the framework of studying the outer surface of reproductive organs. The y mutant peel lacks the yellow flavonoid pigment naringenin chalcone, which has been suggested to influence the characteristics and function of the cuticular layer. Large-scale metabolic and transcript profiling revealed broad effects on both primary and secondary metabolism, related mostly to the biosynthesis of phenylpropanoids, particularly flavonoids. These were not restricted to the fruit or to a specific stage of its development and indicated that the y mutant phenotype is due to a mutation in a regulatory gene. Indeed, expression analyses specified three R2R3-MYB–type transcription factors that were significantly down-regulated in the y mutant fruit peel. One of these, SlMYB12, was mapped to the genomic region on tomato chromosome 1 previously shown to harbor the y mutation. Identification of an additional mutant allele that co-segregates with the colorless-peel trait, specific down-regulation of SlMYB12 and rescue of the y phenotype by overexpression of SlMYB12 on the mutant background, confirmed that a lesion in this regulator underlies the y phenotype. Hence, this work provides novel insight to the study of fleshy fruit cuticular structure and paves the way for the elucidation of the regulatory network that controls flavonoid accumulation in tomato fruit cuticle

BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways

The BOLITA (BOL) gene, an AP2/ERF transcription factor, was characterized with the help of an activation tag mutant and overexpression lines in Arabidopsis and tobacco. The leaf size of plants overexpressing BOL was smaller than wild type plants due to a reduction in both cell size and cell number. Moreover, severe overexpressors showed ectopic callus formation in roots. Accordingly, global gene expression analysis using the overexpression mutant reflected the alterations in cell proliferation, differentiation and growth through expression changes in RBR, CYCD, and TCP genes, as well as genes involved in cell expansion (i.e. expansins and the actin remodeling factor ADF5). Furthermore, the expression of hormone signaling (i.e. auxin and cytokinin), biosynthesis (i.e. ethylene and jasmonic acid) and regulatory genes was found to be perturbed in bol-D mutant leave

Adherence to self-managed exercises for patients with persistent subacromial pain: the Ad-Shoulder feasibility study

© 2021, The Author(s). Background: Exercise is recommended for patients with subacromial pain. It has been suggested that good exercise adherence improves clinical outcomes. Despite this, little attention has been paid to the need for behavioural frameworks to enhance adherence to home exercise programmes for patients with subacromial pain. Methods: A feasibility study with pre-post design was used. Participants aged > 18 years, with subacromial pain, who had received conservative treatment during the past 6 months, were recruited. The Ad-Shoulder intervention consisted of 1–5 individual sessions provided over 3 months and was based on 5 self-management skills, which aimed to enhance the patients’ self-efficacy and adherence to self-managed exercises. The primary objectives were assessed according to predefined progression criteria: (1) the recruitment rate (10 patients enrolled within 12 weeks), (2) follow-up rate (≥ 80% on all self-reported measures), (3) objective physical activity measures (≥ 80% of participants would contribute valid data at each time point), (4) adherence with the self-managed exercises (≥ 80% of the participants would adhere to ≥ 80% of the assigned home exercise programme), (5) fidelity of the delivery of the intervention (the therapists delivered the intervention according to the protocol) and (6) adverse events (< 30% would report adverse events (including mild)). The results were reported using descriptive statistics. Results: Eleven patients were recruited during 16 weeks. Ten patients completed the self-reported measures at baseline and week 12. Objective physical activity measures were successfully obtained for 100% (11/11) at baseline, 64% (7/11) at week six and 82% at week 12. Fifty-five percent (6/11) of the participants satisfactorily completed at least 80% of their home exercise programme. All sessions were delivered according to the protocol. None of the patients reported any adverse events. Conclusions: Objective physical activity data measures at baseline and week 12, follow-up, the physiotherapists’ fidelity to the intervention and adverse events met our pre-specified progression criteria. Recruitment and adherence to the self-managed exercise programme were both below the anticipated level. Further intervention development is necessary to understand whether adherence to the self-managed exercises could be enhanced and additional methods of recruitment would need to be considered, including additional recruitment sites, in any planning for a future main trial. Trial registration: ClinicalTrials.gov, NCT04190836, Registered December 9, 2019—retrospectively registered